It was a fun interview and I love the idea of teens doing a science radio show. From their site

Science is everywhere. From the stars that light the night sky to the intricate patterns on a butterfly’s wings, science is at play in all parts of our world and is continually making our lives so great. Hosts Henna Hundal and Courtney Chung discuss how science shapes our perspective on life from cell phones to lawn mowers, from cures for diseases to prosthetic limbs. Global Youth Talk reporter, Ryan Sim, talks about science careers in the United Nations, and how this international community is looking at science innovation to create solutions for the next generation. Special guest Dr. Jonathan Eisen,a Full Professor at the University of California, Davis, with appointments in the UC Davis Genome Center, the School of Medicine, and the College of Biological Sciences focuses on communities of microbes and how they provide new functions - to each other or to a host. Dr. Eisen is entertaining with his study systems of boiling acid pools, surface ocean waters, agents of many diseases, and the microbial ecosystems in and on plants and animals. In Health with Henna, Henna Hundal reports on how we can prevent the negative effects of prolonged sitting. It’s important to take those “stretch breaks” every hour. Whether it’s writing scientific articles, thoughtful science reporting, or even talking about science on the radio, integrating humanities with science is key to reaching a mass audience.

Monday, September 29, 2014

Well, umm, Ralph Snyderman, despite the email invitation I will not be attending PMWC 2015 Silicon Valley. Why not? Well how about the fact that you have 55 speakers listed, only 7 of which are women.

Previous year's meetings are not much better. For example, for the 2014 Meeting in Silicon Valley the Track 1 session (which they call the premier session or something like that) has a ratio of 52:5 Male:Female.

Wednesday, September 24, 2014

Elizabeth Bik sent me a link to this meeintg: DRUG DISCOVERY & THERAPY WORLD CONGRESS 2015 with a comment about the ratio of males to females in the keynote speakers. And it is painful. Of the plenary and keynote speakers, 15 are male and 1 is female. Below I show pics of the plenary and keynote speakers:

Plenary and Keynote Speakers at Drug Discovery and Thearpy World Congress

Female Plenary and Keynote Speakers at Drug Discovery and Thearpy World Congress

Two bonus people who could have been giving keynote talks but who actually are not.

Well, this is one of the strangest and lamest things I have seen associated with a conference in a while. Elizabeth Bik just emailed me to show me an invite she received to the "Global Biotechnology Congress 2015." And here is the bizarre thing. It is at the same time as the Drug Discovery meeting discussed here. Same place. Same speakers. It is apparently the same meeting with a new name.

Same bad gender ratio of course too.

Did they do this to avoid people discovering my post about the awful gender ratio? I don't know but seems like it might be so. What a joke. Well, I can guarantee people will associated this meeting name with the previous one.

Here is another post in my "Story Behind the Paper" series where I ask authors of open access papers to tell the story behind their paper. This one comes from Rogan Carr and Elhanan Borenstein. Note - this was crossposted at microBEnet. If anyone out there has an open access paper for which you want to tell the story -- let me know.

We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct functional annotation of short metagenomic reads that stemmed from protocol development for our lab. Jon invited us to write a blog post on the subject, and we thought it would be a great venue to discuss some practical applications of our work and to share with the research community the motivation for our study and how it came about.

Our lab, the Borenstein Lab at the University of Washington, is broadly interested in metabolic modeling of the human microbiome (see, for example our Metagenomic Systems Biology approach) and in the development of novel computational methods for analyzing functional metagenomic data (see, for example, Metagenomic Deconvolution). In this capacity, we often perform large-scale analysis of publicly available metagenomic datasets as well as collaborate with experimental labs to analyze new metagenomic datasets, and accordingly we have developed extensive expertise in performing functional, community-level annotation of metagenomic samples. We focused primarily on protocols that derive functional profiles directly from short sequencing reads (e.g., by mapping the short reads to a collection of annotated genes), as such protocols provide gene abundance profiles that are relatively unbiased by species abundance in the sample or by the availability of closely-related reference genomes. Such functional annotation protocols are extremely common in the literature and are essential when approaching metagenomics from a gene-centric point of view, where the goal is to describe the community as a whole.

However, when we began to design our in-house annotation pipeline, we pored over the literature and realized that each research group and each metagenomic study applied a slightly different approach to functional annotation. When we implemented and evaluated these methods in the lab, we also discovered that the functional profiles obtained by the various methods often differ significantly. Discussing these findings with colleagues, some further expressed doubt that that such short sequencing reads even contained enough information to map back unambiguously to the correct function. Perhaps the whole approach was wrong!

We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample. We specifically decided to pursue a large-scale study, performed as rigorously as possible, taking into account both the phylogeny of the microbes in the sample and the phylogenetic coverage of the database, as well as several technical aspects of sequencing like base-calling error and read length. We have found this evaluation approach and the results we obtained quite useful for designing our lab protocols, and thought it would be helpful to share them with the wider metagenomics and microbiome research community. The result is our recent paper in PLoS One, Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads.

Saturday, September 20, 2014

Well sometimes you just screw up. In 2007 I attended some planning meetings for the human microbiome project (see for example A human microbiome program? a post I wrote from one of the meetings in 2007). And at those meetings I kept asking one question. Where did this "fact" everyone kept citing that there were "10 times as many microbial cells in the human body as there were human cells" come from? I could not find a citation. So I started taking some notes for a blog post about this. Here are those notes:

Wikipedia linkOnline textbook hereSears paper from Arizona site. She discusses only gut bacteria and cites a Gordon paper from 2001.Seems to not be from this paper but really from here:This in turn is not from there but apparently here

But, alas I got distracted. And I did keep asking people - where did this "fact" come from. And most people just brushed me off (and probably thought I was a bit of a crank ...). And nobody had a good answer. Well, I was both pleased and sad (because I should have done it) to see Is your body mostly microbes? Actually, we have no idea by Peter Andrey Smith in the Boston Globe who addresses this issue in much much more detail that I ever could have done. Everyone who works on the human microbiome and who is interested in "facts" and how they can get misreported should read this. As a side note, Smith reports in the article that this is even given as a fact in Ted talks. Sadly mine was one of them. This is despite the fact (yes, the fact) that I swore to myself that I would NOT say that in my talk since I have been such a crank about this issue at meetings. OMG - such truisms are so pervasive that even someone who actively questioned the truism still used it. Uggh. Oh well. I really should have finished that draft post.

Friday, September 19, 2014

As many know, I spend a decent amount of effort critiquing conferences that have poor speaker diversity (mostly focus on gender ratio). Well I am also trying to start calling out in a positive way those meetings that do a good job with speaker diversity. And here is one: 2014 Xenopus Genetics meeting in Pacific Grove. I was pointed to it in an email that was in response to a Tweet I posted (not sure if I have permission to say who this was from - will post if they say it is OK). (UPDATE 9/20 - it was Ian Quigley).

From what I compute - the ratio was 30:22 male: female. I do not know what the ratio of the "pool" of speakers is but regardless, having 42% female speakers is a more even ratio than I have seen for most life sciences meetings. So they deserve some props for this.Female speakers highlighted in yellow. Male in green.

And though there was a bit of a discussion on Twitter I felt I had to follow up with a blog post. When I saw the post I was at a conference (Lake Arrowhead Microbial Genomes) where I could get Twitter access but for some reason very little web access. So I could not dig around until now (I am home).

This meeting is a complete disgrace and an embarassment for the field of evolutionary biology, for the University of Cambridge which is hosting the meeting, and for the Templeton Foundation which is sponsoring it.

Notice anything now? How about I help you some more by masking out the men and not the women.

Impressive no? 25 speakers - 23 of them male. I guess that means there are no qualified female speakers who coudl discuss something about evolution right? It would be worth reading "Fewer invited talks bu women in evolutionary biology symposia" to get some context. What an incredible, disgusting, distasteful and disgraceful meeting.

I recommend to everyone who was considering going to this meeting - skip it. Also consider writing to the University of Cambirdge and the Templeton Foundation to express your thoughts about the meeting. This certainly is a fine example of Yet Another Mostly Male Meeting (YAMMM). Well, maybe I should word that differently - this is a disgusting example of a YAMMM.

Sunday, September 14, 2014

The Lake Arrowhead Microbial Genomes meeting, which happens every other year, is starting tonight. I love this meeting. No bias here since I am now a co-organizer. But I really love this meeting. I am posting here some background information about the meeting for those interested. We will be live tweeting the meeting using the hashtag #LAMG14. This years program is here.

Anyway - enough about me - what about this paper? It has so many nuggets of interest I am not sure which to highlight so I will just go through some of it. Oh - and it is published with a Creative Commons Attribution license (yay).

Abstract: While scientists are often exhorted to write better, it isn’t entirely obvious what “better” means. It’s uncontroversial that good scientific writing is clear, with the reader’s understanding as effortless as possible. Unsettled, and largely undiscussed, is the question of whether our goal of clarity precludes us from making our writing enjoyable by incorporating touches of whimsy, humanity, humour, and beauty. I offer examples of scientific writing that offers pleasure, drawing from ecology and evolution and from other natural sciences, and I argue that enjoyable writing can help recruit readers to a paper and retain them as they read. I document resistance to this idea in the scientific community, and consider the objections (well grounded and not) that may lie behind this resistance. I close by recommending that we include touches of whimsy and beauty in our own writing, and also that we work to encourage such touches in the writing of others.

OK - the title would have drawn me in anyway but the abstract definitely had me.

Heard documents a bit of a spat between Sprat and Boyle from the 1660s regarding scientific writing. I especially like the Boyle quote:

To affect needless rhetorical ornaments in setting down an experiment...were little less improper than...to paint the eyeglasses of a telescope...in which even the most delightful colours cannot so much please the eye as they would hinder the sight...And yet I approve not that dull and insipid way of writing, which is practiced by many...for though a philosopher need not be solicitous that his style should delight his reader with his floridness, yet I think he may very well be allowed to take a care that it disgust not his reader by its flatness...Though it were foolish to colour...the glasses of telescopes, yet to gild...the tubes of them may render them most acceptable to the users (Boyle 1661:11-12, spelling and punctuation modern- ized).

Heard then goes through some different aspects of good scientific writing

Sightings (1): Playfulness in the scientific literature

Sightings (2): Beauty

Also - he then doscusses pushback against the "notion that whimsy, jokes, and beauty can have a place in our scientific literature." which I have also seen in many contexts.

He ends with suggestions and I quote the whole section with some highlights:

If you write papers that are crystal clear and thus effortless to read, you’ll have achieved the primary goal of scientific writing and your work will be among the best of our literature. But if you want to reach for even more, if you agree with me that we can also offer our readers some pleasure in reading, what can you do? To begin, you can try to write with small touches of whimsy, humanity, humour, and beauty—without, of course, compromising clarity; and even knowing that sometimes, reviewers will make you take them out. I am not suggesting writing in which art shares the stage equally with content (as can be true in the lay literature). Rather, the goal that’s within our reach is clear, functional writing punctuated with occasional nuggets of playfulness or glints of beauty—to extend Boyle’s metaphor, not a telescope of solid gold but one lightly gilded.

You can also work to encourage pleasure in what your colleagues write, in two complementary ways. First, when you review manuscripts, you can suppress the reflex telling you to question any touches of whimsy, humour, or beauty that you find; you can even (gently) suggest some be put in. Second, you can announce your admiration of writing that has given you pleasure. Announce your admiration to the writers who crafted the passage, to editors who might be considering its fate, and to students or colleagues who might read it. If we choose to, we can change our culture to deliver, and value, pleasure along with function in our writing.

This is a must read paper. And I really wish more people would endorse the idea that scientific writing can include more than just science. Of course, there are many who already endorse this notion but for those who do not - give it a try.

Bonnie Baxter and Nina Gunde-Cimerman at the north arm of Great Salt Lake (2008)

I was drawn to the western US, the extreme landscapes, and ended up at the only liberal arts college in Utah. I had wanted a career doing science with undergraduates, and I set about exploring the microbiota of Great Salt Lake. Since few had studied this incredible spot, I quickly became the go-to person for studies on the lake, and these collaborations and grant projects eventually evolved into an organization I direct called Great Salt Lake Institute. We are dedicated to research, scholarship and education efforts on Great Salt Lake.

There had been no microbiology done on Great Salt Lake since 1979. This is why there was much excitement concerning our emerging data, and in 2004, I was invited to speak at the triennial International Halophiles conference in Slovenia. Halophiles are microbes that thrive at high-salt, and the people who study them maintain an interesting balance of field-work and lab work. I had been to large meeting on DNA repair, DNA replication, nucleases and the like, but I had never met a group who were centered on a theme that connected them around the planet.

From my first Halophiles meeting (I’ve since attended 2007 in Colchester UK, 2010 in Beijing and 2013 at University of Connecticut), I felt an unusual level of support from the elders of this group. And I noticed that, unlike the NASA meetings or biochemistry meetings I attended, there seemed to be a nice balance of men and women. There were a group of folks who had participated for a long time, without a membership organization, and these people maintained the notion of mentoring in the field. It is this spirit that drew all of us younger folk to participate.

Friday, September 05, 2014

So I am going to make this simple here. Paperwork at UC Davis is driving me batty these days. One thing in particular does not make much sense to me. When I or anyone who works in my lab go on trips associated with work, we have to collect all the receipts for the trip and then these need to be submitted in an intemized way for reimbursement. With a lot of people going on a lot of trips, this amounts to a lot of work for us, for my administrative assistant, for the UC Davis Genome Center administration, and for the UC administration. At other places I have worked, and in other situations, people can get reimbursed using a per diem calculation. Such calculations save an absurd amount of work for people even if they come with some "risks" such as people getting reimbursed for more than they actually spent. Personally, I would take a 50% per diem to save everyone the trouble associated with all the reciepts and submitting them and checking them and such.

So - the reason I am writing is to ask - what happens at other institutions? Does everyone have to submit all the receipts? Or does anyone out there do per diems?

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”

And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today: Don’t ignore the science Davis Enterprise. I quote from it below:

The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.”

Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?

He completely nailed it here. I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.

Tuesday, September 02, 2014

Well, this is a new one for me and my family. We got some mail today. My wife called me over this evening to tell me and said "it might make something good for my blog". But it was very strange. From the US Postal Service. In a plastic bag and the bag read "We care ..." see below:

And inside of this was half of a piece of mail. A card. It felt very weird. Like someone was censoring us but most likely some machine just ate the other half.

Front

Back

Add caption

They easily could have just tossed this once it got damaged. Glad they did this. Now, mind you, I still detest all their junk mail / bulk mail policies, but this was nice ..

We take great delight in inviting you to join the Editorial Board for the Journal of HIV/AIDS , which is an open access, peer reviewed journal managed by Sci Forschen. Ensuring quality and accuracy for every submitted article is the top most priority for Sci Forschen, and we genuinely believe that someone with the knowledge and experience, such as yourself, can really make a huge difference for us.

Journal of HIV/AIDS , publishes cutting edge research work submitted by scholars from all over the world, and we believe that your presence will polished up with the help of illustrious experts in research field.

We are always striving to involve eminent personalities like you and your standing in the global community makes us confident.

Kindly let us know your valuable response and acceptance if possible with in 48 hours.